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<div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;">Hi Michael,</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;"><br>
</div>
<div><font face="Calibri,sans-serif" style="font-size: 14px;">Nice idea. Especially motorising the corner mirrors as it would also make an ‘autofocus’ function during each z-step possible. Not just for the air/immersion fluid mismatch, but for RI inconsistencies
throughout cleared samples as was done in ‘CLARITY optimised light sheet microsc</font>opy’ (COLM – Tomer et al., <i>Nat Protoc</i> 9(7), 2014).</div>
<div><br>
</div>
<div>Luckily most of the immersion fluids for CLARITY are fairly innocuous, so the dipping objectives should be fine. Although I’m not sure how the dipping objectives would fare with the organic solvents used in techniques like BABB or 3DISCO…</div>
<div><br>
</div>
<div>Cheers</div>
<div>Jamie</div>
</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;"><br>
</div>
<span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif;">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span><<a href="mailto:openspim-bounces@openspim.org">openspim-bounces@openspim.org</a>> on behalf of Michael Weber <<a href="mailto:weber@mpi-cbg.de">weber@mpi-cbg.de</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 26 October 2015 5:16 am<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>" <<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [OpenSPIM] OpenSPIM and optically cleared 3D tissue<br>
</div>
<div><br>
</div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Hi Jamie,</div>
<div><br>
</div>
<div>if you are using hazardous clearing media and don't have a dedicated dipping objective available, one idea would be to use long-working distance air objectives and a smaller, closed glass chamber. The main issue I would expect from such a combination would
be a drift of your detection focal plane when moving the sample through the light sheet, because the light has to travel through layers of different refractive indices, and you change the "thickness" of those layers. But this drift should be linear and could
be corrected by adapting the distance between light sheet and detection objective while acquiring a z-stack. So you would either need to motorize the mirror for translating the light sheet, or your detection objective, and then implement the drift correction
in the software. Might be worth a try, unless I overlooked something important here.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Michael</div>
<br>
<div>
<div>On Oct 24, 2015, at 8:27 AM, Jamie Flynn <<a href="mailto:Jamie.Flynn@uon.edu.au">Jamie.Flynn@uon.edu.au</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi Pete,<br>
<br>
Thanks for the link. Some very impressive images from the mesolens. You¹re<br>
right that pickings are slim for commercially available lenses. Leica and<br>
Olympus have some objectives that are suitable for various types of<br>
cleared tissue, but come with hefty price tags. Apparently Zeiss have<br>
something in the works as well (not that it¹ll be cheap!). The RI range of<br>
imaging media for different clearing techniques is obviously one of the<br>
bigger challenges (e.g. 1.45 for Focusclear and 1.56 for DBE). Will look<br>
into a custom design as you suggest.<br>
<br>
Cheers<br>
Jamie<br>
<br>
<br>
<br>
On 23/10/2015 7:16 pm, "Peter Gabriel Pitrone" <<a href="mailto:pitrone@mpi-cbg.de">pitrone@mpi-cbg.de</a>> wrote:<br>
<br>
<blockquote type="cite">with the exeption of the "Meso-lens" from Prof. Brad Amos... But I'm sure<br>
it uses glue, and you probably can not afford it.<br>
<br>
<a href="http://www2.mrc-lmb.cam.ac.uk/research/technology-transfer/mesolens-micros">http://www2.mrc-lmb.cam.ac.uk/research/technology-transfer/mesolens-micros</a><br>
copy/<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: "Peter Gabriel Pitrone" <<a href="mailto:pitrone@mpi-cbg.de">pitrone@mpi-cbg.de</a>><br>
To: "Jamie Flynn" <<a href="mailto:Jamie.Flynn@uon.edu.au">Jamie.Flynn@uon.edu.au</a>><br>
Cc: <a href="mailto:openspim@openspim.org">openspim@openspim.org</a><br>
Sent: Friday, October 23, 2015 10:14:06 AM<br>
Subject: Re: [OpenSPIM] OpenSPIM and optically cleared 3D tissue<br>
<br>
Hey Jamie,<br>
<br>
I would have someone design the lenses (and therefor chamber as well) for<br>
you made in a way the is fluid/liquid proof WITHOUT using glue, also<br>
keeping in mind the absolute largest (NA in terms of detection lens, and)<br>
working distance possible so you could put in bigger tissues. I doubt<br>
that there is a objective on the market that would meet your requirements.<br>
<br>
Regards,<br>
Pete<br>
<br>
----- Original Message -----<br>
From: "Jamie Flynn" <<a href="mailto:Jamie.Flynn@uon.edu.au">Jamie.Flynn@uon.edu.au</a>><br>
To: <a href="mailto:openspim@openspim.org">openspim@openspim.org</a><br>
Sent: Friday, October 23, 2015 1:58:29 AM<br>
Subject: [OpenSPIM] OpenSPIM and optically cleared 3D tissue<br>
<br>
Hi everyone, <br>
<br>
We¹re building a dual illumination OpenSPIM at the Hunter Medical<br>
Research Institute in Newcastle, Australia. Our ai m is to have the scope<br>
and analysis pipeline used as a core facility for lab groups to image 3D<br>
tumour cell cultures, developing embryos and most importantly for us,<br>
optically cleared 3D tissue samples (e.g. CLARITY, CUBIC, 3DISCO, Scale<br>
etc.). Imaging cleared 3D samples would be an interesting avenue for<br>
OpenSPIM and it¹d be great to hear about any hardware modifications or<br>
mounting protocols others may have used to do it.<br>
<br>
If anyone wants to try clearing out their own tissue samples, my<br>
colleagues and I put together a handbook that describes the reagents,<br>
equipment and detailed protocols for ŒPassive CLARITY¹. We compiled the<br>
protocols outlined in Tomer et al. Nat. Prot. 9(7) 2014 and Yang et al.<br>
Cell (158) 2014 and added in our own refinements (after much trial and<br>
error!). It¹s a very simple technique and has worked really well in our<br>
hands. Here¹s the link. Download it to your desktop in case the link gets<br>
broken: <br>
<br>
<a href="https://drive.google.com/open?id=0BzIZDgZFR2srNFk2dHFqT1UycFk">https://drive.google.com/open?id=0BzIZDgZFR2srNFk2dHFqT1UycFk</a><br>
<br>
All the best <br>
--------------------<br>
Jamie Flynn (PhD) <br>
University of Newcastle<br>
Hunter Medical Research Institute<br>
Room 3613 level 3 east<br>
1 Kookaburra Circuit, New Lambton Heights<br>
NSW 2305, Australia.<br>
pH: +612 40420468 <br>
Mobile: +61 416003787<br>
Email: <a href="mailto:jamie.flynn@uon.edu.au">jamie.flynn@uon.edu.au</a><br>
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_____________<br>
<br>
Michael Weber<br>
Postdoc, Huisken lab<br>
Max Planck Institute of Molecular Cell Biology and Genetics<br>
Pfotenhauerstrasse 108, 01307 Dresden<br>
Tel. 0049 351/2102837<br>
<br>
<a href="http://www.mpi-cbg.de/huisken">http://www.mpi-cbg.de/huisken</a></div>
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